BackgroundAlthough many computational methods have been developed to predict protein subcellular localization, most of the methods are limited to the prediction of single-location proteins. Multi-location proteins are either not considered or assumed not existing. However, proteins with multiple locations are particularly interesting because they may have special biological functions, which are essential to both basic research and drug discovery.ResultsThis paper proposes an efficient multi-label predictor, namely mGOASVM, for predicting the subcellular localization of multi-location proteins. Given a protein, the accession numbers of its homologs are obtained via BLAST search. Then, the original accession number and the homologous accession numbers of the protein are used as keys to search against the Gene Ontology (GO) annotation database to obtain a set of GO terms. Given a set of training proteins, a set of T relevant GO terms is obtained by finding all of the GO terms in the GO annotation database that are relevant to the training proteins. These relevant GO terms then form the basis of a T-dimensional Euclidean space on which the GO vectors lie. A support vector machine (SVM) classifier with a new decision scheme is proposed to classify the multi-label GO vectors. The mGOASVM predictor has the following advantages: (1) it uses the frequency of occurrences of GO terms for feature representation; (2) it selects the relevant GO subspace which can substantially speed up the prediction without compromising performance; and (3) it adopts an efficient multi-label SVM classifier which significantly outperforms other predictors. Briefly, on two recently published virus and plant datasets, mGOASVM achieves an actual accuracy of 88.9% and 87.4%, respectively, which are significantly higher than those achieved by the state-of-the-art predictors such as iLoc-Virus (74.8%) and iLoc-Plant (68.1%).ConclusionsmGOASVM can efficiently predict the subcellular locations of multi-label proteins. The mGOASVM predictor is available online at http://bioinfo.eie.polyu.edu.hk/mGoaSvmServer/mGOASVM.html.

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Since 2008, interview-style speech has become an important part of the NIST Speaker Recognition Evaluations (SREs). Unlike telephone speech, interview speech has lower signal-to-noise ratio, which necessitates robust voice activity detectors (VADs). This paper highlights the characteristics of interview speech files in NIST SREs and discusses the difficulties in performing speech/non-speech segmentation in these files. To overcome these difficulties, this paper proposes using speech enhancement techniques as a preprocessing step for enhancing the reliability of energy-based and statisticalmodel-based VADs. A decision strategy is also proposed to overcome the undesirable effects caused by impulsive signals and sinusoidal background signals. The proposed VAD is compared with the ASR transcripts provided by NIST, VAD in the ETSI-AMR Option 2 coder, satistical-model (SM) based VAD, and Gaussian mixture model (GMM) based VAD. Experimental results based on the NIST 2010 SRE dataset suggest that the proposed VAD outperforms these conventional ones whenever interview-style speech is involved. This study also demonstrates that (1) noise reduction is vital for energy-based VAD under low SNR; (2) the ASR transcripts and ETSI-AMR speech coder do not produce accurate speech and non-speech segmentations; and (3) spectral subtraction makes better use of background spectra than the likelihood-ratio tests in the SM-based VAD. The segmentation files produced by the proposed VAD can be found in http://bioinfo.eie.polyu.edu.hk/ssvad.

Prediction of protein subcellular localization is an important yet challenging problem. Recently, several computational methods based on Gene Ontology (GO) have been proposed to tackle this problem and have demonstrated superiority over methods based on other features. Existing GO-based methods, however, do not fully use the GO information. This paper proposes an efficient GO method called GOASVM that exploits the information from the GO term frequencies and distant homologs to represent a protein in the general form of Chou's pseudo amino acid composition. The method first selects a subset of relevant GO terms to form a GO vector space. Then for each protein, the method uses the accession number (AC) of the protein or the ACs of its homologs to find the number of occurrences of the selected GO terms in the Gene Ontology annotation (GOA) database as a means to construct GO vectors for support vector machines (SVMs) classification. With the advantages of GO term frequencies and a new strategy to incorporate useful homologous information, GOASVM can achieve a prediction accuracy of 72.2% on a new independent test set comprising novel proteins that were added to Swiss-Prot six years later than the creation date of the training set. GOASVM and Supplementary Materials are available online at

The performance of telephone-based speaker verification systems can be severely degraded by the acoustic mismatch caused by telephone handsets. This paper proposes to combine a handset selector with stochastic feature transformation to reduce the mismatch. Specifically, a GMM-based handset selector is trained to identify the most likely handset used by the claimants, and then handset-specific stochastic feature transformations are applied to the distorted feature vectors. To overcome the non-linear distortion introduced by telephone handsets, a 2nd-order stochastic feature transformation is proposed. Estimation algorithms based on the stochastic matching technique and the EM algorithm are derived. Experimental results based on 150 speakers of the HTIMIT corpus show that the handset selector is able to identify the handsets accurately (98.3%), and that both linear and non-linear transformation reduce the error rate significantly (from 12.37% to 5.49%).

Protein subcellular localization prediction, as an essential step to elucidate the functions in vivo of proteins and identify drugs targets, has been extensively studied in previous decades. Instead of only determining subcellular localization of single-label proteins, recent studies have focused on predicting both single- and multi-location proteins. Computational methods based on Gene Ontology (GO) have been demonstrated to be superior to methods based on other features. However, existing GO-based methods focus on the occurrences of GO terms and disregard their relationships. This paper proposes a multi-label subcellular-localization predictor, namely HybridGO-Loc, that leverages not only the GO term occurrences but also the inter-term relationships. This is achieved by hybridizing the GO frequencies of occurrences and the semantic similarity between GO terms. Given a protein, a set of GO terms are retrieved by searching against the gene ontology database, using the accession numbers of homologous proteins obtained via BLAST search as the keys. The frequency of GO occurrences and semantic similarity (SS) between GO terms are used to formulate frequency vectors and semantic similarity vectors, respectively, which are subsequently hybridized to construct fusion vectors. An adaptive-decision based multi-label support vector machine (SVM) classifier is proposed to classify the fusion vectors. Experimental results based on recent benchmark datasets and a new dataset containing novel proteins show that the proposed hybrid-feature predictor significantly outperforms predictors based on individual GO features as well as other state-of-the-art predictors. For readers' convenience, the HybridGO-Loc server, which is for predicting virus or plant proteins, is available online at http://bioinfo.eie.polyu.edu.hk/HybridGoServer/.

In real-world environments, noisy utterances with variable noise levels are recorded and then converted to i-vectors for cosine distance or PLDA scoring. This paper investigates the effect of noise-level variability on i-vectors. It demonstrates that noise-level variability causes the i-vectors to shift, causing the noise contaminated i-vectors to form clusters in the ivector space. It also demonstrates that optimal subspaces for discriminating speakers are noise-level dependent. Based on these observations, this paper proposes using signal-to-noise ratio (SNR) of utterances as guidance for training mixture of PLDA models. To maximize the coordination among the PLDA models, mixtures of PLDA models are trained simultaneously via an EM algorithm using the utterances contaminated with noise at various levels. For scoring, given a test i-vector, the marginal likelihoods from individual PLDA models are linearly combined by the posterior probabilities of the test utterance's SNR. Verification scores are the ratio of the marginal likelihoods. Results based on NIST 2012 SRE suggest that the SNR-dependent mixture of PLDA is not only suitable for the situations where the test utterances exhibit a wide range of SNR, but also beneficial for the test utterances with unknown SNR distribution. Supplementary materials containing full derivations of the EM algorithms and scoring functions can be found in http://bioinfo.eie.polyu.edu.hk/mPLDA/SuppMaterials.pdf.

Abstract-The success of the recent i-vector approach to speaker verification relies on the capability of i-vectors to capture speaker characteristics and the subsequent channel compensation methods to suppress channel variability. Typically, given an utterance, an i-vector is determined from the utterance regardless of its length. This paper investigates how the utterance length affects the discriminative power of i-vectors and demonstrates that the discriminative power of i-vectors reaches a plateau quickly when the utterance length increases. This observation suggests that it is possible to make the best use of a long conversation by partitioning it into a number of sub-utterances so that more ivectors can be produced for each conversation. To increase the number of sub-utterances without scarifying the representation power of the corresponding i-vectors, repeated applications of frame-index randomization and utterance partitioning are applied. Results on NIST 2010 speaker recognition evaluation (SRE) suggest that (1) using more i-vectors per conversation can help to find more robust linear discriminant analysis (LDA) and withinclass covariance normalization (WCCN) transformation matrices, especially when the number of conversations per training speaker is limited; and (2) increasing the number of i-vectors per target speaker helps the i-vector based support vector machines (SVM) to find better decision boundaries, thus making SVM scoring outperforms cosine distance scoring by 19% and 9% in terms of minimum normalized DCF and EER.